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Enterococci and coliforms isolated from soils amended with manure and digestate
To provide a hub for research into environmental transmission and survival of human and animal pathogens through which a strong network will be developed both within Scotland and globally, with the aim of being prepared and equipped to address any future research challenges in this area.

The core research group in the Centre for Human and Animal Pathogens in the Environment (HAP-E) at the James Hutton Institute studies the following pathogen-environment systems.

  • Transmission of antimicrobial resistance through environmental matrices
  • Prevalence and survival of pathogens in  the environment: waters, soils, plants, slurries, manures, anaerobic digestate and feedstocks, compost
  • Mitigation measures against faecal point source and diffuse pollution from agriculture and human sewage.
  • Faecal indicator organisms - transmission through catchments and interactions with particles
    Source tracking of faecal pollution
  • Pathogen removal and survival during anaerobic digestion processes in the UK and Africa.

We are investigating a wide range of pathogenic species; however we have particular interests in E. coli, Mycobacterium avium paratuberculosis, Clostridium and Salmonella

HAP-E acts as a hub through which we link with associate members from other research institutions and with national and international collaborators to provide a critical mass of knowledge and expertise in the field of environment-associated pathogens. Through shared research platforms, resources, approaches, and ideas, we are able to address key fundamental questions on human and animal pathogens in the environment.

Key questions

  • What are the intrinsic biological (genotypic and phenotypic) characteristics influencing bacterial transmission in soil and aquatic systems?
  • What role does the environment play in transmission and development of antimicrobial resistance?
  • What are the risks to humans and animals from bacteria entering the food chain via the environment?
  • What are the mechanisms that underpin the interactions between human pathogens and plants?
  • What is the likelihood of transmission of human pathogens to crop plants?
  • What methodologies can we exploit to detect and differentiate pathogens in the environment?
  • How do we address the gaps in our knowledge with respect to pathogen persistence in the environment?


Areas of Interest

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.